The question is not just what's to be done but who's to decide. That's what the prime directive is at its heart all about: preventing individuals with great power from deciding what will happen to civilizations with less. The prime directive puts most day-to-day decisions in the hands of alien civilizations, not the powerful humans (and their allies) who study them. It also ensures that the trickiest decisions will be referred to a body more diverse and deliberative than an individual captain. Even in the case of most natural disasters, it should really be the call of higher Starfleet authorities, not an individual captain, if the prime directive should be suspended. Of course, you can pose some hypothetical or write some story where a captain is called upon to make some snap decision when an entire species' extinction hangs in the balance, but the prime directive is meant to govern the more likely and more typical situations. In the extreme ones, a good captain like Kirk can make his best guess (as he did in Into Darkness) and then take responsibility for the consequences (as he tried not to do in Into Darkness).
But the problem is, you have episodes where Janeway or Picard argue its the moral thing to do, to let civilizations be destroyed by natural disasters. How is that the moral thing to do?
Why do Janeway and Picard think that is the moral thing to do, why does the PD make exceptions for saving civilizations from natural disasters? I'm not saying they have to stop every natural disaster in the universe, but if they find a situation where they can save civilization from a natural disaster, with just some effort, then what is wrong with doing that?
I don't see how Federation is denying civilization self determination, if they are saving it from a natural disaster, it seems like doing that, would give this civilization its self determination, because they would still be alive. You can't really deny self determination or "ruin" a civilization that will be destroyed anyway, so that is not a logical argument.
I'm not saying the Federation should stop wars or remove dictators by force, those are trickier situations, with a lot of fallout, but stopping natural disasters seems easier and should be uncontroversial.
This is why a lot of people don't like more modern PD stories, it went from something reasonable to somewhat that is dogmatic and inflexable and something that people take to ridclius extremes.
If 4 million people die in one day from one natural disaster, steps are taken to make sure that next time around, Alien-FEMA isn't run by dipshits, or they stop building tenements on faultlines, or just in general the survivors are a little more weary of dirty telephones.
Stumbling and falling on your face is an important part of learning and growing and maturing.
What if everyone dies due to a natural disaster on a planet, what lessons are learned there? The problem is we have had episodes like these, Pen Pals and Homeward, where an entire civilization is going to be destroyed by a natural disaster and Picard says the moral thing to do is to let them die. How is that logical?
That just seems like laziness, callousness and moral cowardice.